Setup

Load R libraries

library(data.table)
library(ggplot2)
library(ggpubr)
library(tidyr)
library(limma)
library(biomaRt)
library(fgsea)
library(goseq)

theme_set(theme_classic())

cell_type_name = params$cell_type_name
graph_weight = params$graph_weight

cell_type_name
## [1] "Astro"
graph_weight
## [1] "5.0"

Check enrichment of gene sets

Read in gene info and gene set assignments

file_tag = sprintf("%s_%s", cell_type_name, graph_weight)

assayed_genes = scan(sprintf("output/gene_list_%s.txt", file_tag), 
                     what = character(), sep="\n")

gene_sets = scan(sprintf("output/name_s_%s.txt", file_tag), 
                 what = character(), sep="\n")

gene_sets = sapply(gene_sets, strsplit, split=",")
n_genes   = sapply(gene_sets, length)
names(n_genes) = NULL
summary(n_genes)
##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
##      41      43      44      44      45      46
length(n_genes)
## [1] 40
sort(n_genes)
##  [1] 41 41 42 42 43 43 43 43 43 43 43 43 43 43 44 44 44 44 44 44 44 45 45 45 45
## [26] 45 45 45 45 45 45 45 45 45 45 45 45 45 45 46

Find gene symbols

Find gene symbols from bioMart.

All the gene symbols that can be found in bioMart are consistent with what we have. So no need to run it.

ensembl = useMart("ensembl", dataset = "hsapiens_gene_ensembl")

gene_BM = getBM(attributes = c("hgnc_symbol", "external_gene_name"), 
                filters = "external_gene_name", 
                values = assayed_genes, 
                mart = ensembl)
length(assayed_genes)
dim(gene_BM)
gene_BM[1:2,]

table(assayed_genes %in% gene_BM$external_gene_name)

t1 = table(gene_BM$external_gene_name)
dup = names(t1)[t1 > 1]
gene_BM[gene_BM$external_gene_name %in% dup,]

table(gene_BM$hgnc_symbol == gene_BM$external_gene_name)
w2kp = which(gene_BM$hgnc_symbol != gene_BM$external_gene_name)
gene_BM[w2kp,]

Find gene symbols using the alias2Symbol function from limma.

a2s = rep(NA, length(assayed_genes))
for(i in 1:length(assayed_genes)){
  gi = assayed_genes[i]
  ai = alias2Symbol(gi)
  if(length(ai) > 1){
    print(gi)
    print(ai)
  }
  a2s[i] = ai[1]
}
## [1] "MPP6"
## [1] "MPHOSPH6" "PALS2"
table(is.na(a2s))
## 
## FALSE  TRUE 
##  1643   357
table(a2s == assayed_genes, useNA = 'ifany')
## 
## FALSE  TRUE  <NA> 
##    21  1622   357
gene_info = data.table(sym_in_data = assayed_genes, sym_limma = a2s)

gene_info[sym_in_data != sym_limma,]
##      sym_in_data   sym_limma
##  1:       BTBD11       ABTB3
##  2:    LINC01006    RNF32-DT
##  3:    LINC01185      REL-DT
##  4:   ZRANB2-AS2   ZRANB2-DT
##  5:    LINC00271     AHI1-DT
##  6:     RFX3-AS1     RFX3-DT
##  7:    COX10-AS1    COX10-DT
##  8:   SUCLG2-AS1   SUCLG2-DT
##  9:      C5orf17   LINC02899
## 10:     OSMR-AS1     OSMR-DT
## 11:  C8orf37-AS1 CFAP418-AS1
## 12: CTB-178M22.2   TENM2-AS1
## 13:    LINC00637 PPP1R13B-DT
## 14:         MPP6    MPHOSPH6
## 15:      C7orf61      SPACDR
## 16:      C3orf35       APRG1
## 17:       HRAT92    PDGFA-DT
## 18:    LINC00884  ATP13A3-DT
## 19:    LINC01137  ZC3H12A-DT
## 20: TMEM161B-AS1 TMEM161B-DT
## 21:      MAFG-DT       MILIP
##      sym_in_data   sym_limma
gene_info[, gene_symbol := sym_in_data]
gene_info[which(sym_in_data != sym_limma & (gene_symbol != "MT-CO2")), 
                gene_symbol := sym_limma]

dim(gene_info)
## [1] 2000    3
gene_info[1:5,]
##    sym_in_data sym_limma gene_symbol
## 1:        CD38      CD38        CD38
## 2:     PRKAR2B   PRKAR2B     PRKAR2B
## 3:        ASB4      ASB4        ASB4
## 4:       USH1C     USH1C       USH1C
## 5:    ARHGAP44  ARHGAP44    ARHGAP44
t1 = table(gene_info$gene_symbol)
table(t1)
## t1
##    1 
## 2000

Prepare gene set information

Gene set annotations (by gene symbols) were downloaded from MSigDB website.

gmtfile = list()
gmtfile[["reactome"]] = "../Annotation/c2.cp.reactome.v2023.2.Hs.symbols.gmt"
gmtfile[["go_bp"]]    = "../Annotation/c5.go.bp.v2023.2.Hs.symbols.gmt"

pathways = list()
for(k1 in names(gmtfile)){
  pathways[[k1]] = gmtPathways(gmtfile[[k1]])
}

names(pathways)
## [1] "reactome" "go_bp"
sapply(pathways, length)
## reactome    go_bp 
##     1692     7647

Filter gene sets for size between 10 and 500.

lapply(pathways, function(v){
  quantile(sapply(v, length), probs = seq(0, 1, 0.1), na.rm = TRUE)
})
## $reactome
##     0%    10%    20%    30%    40%    50%    60%    70%    80%    90%   100% 
##    5.0    7.0    9.0   12.0   17.0   23.0   31.0   44.0   71.8  120.9 1463.0 
## 
## $go_bp
##     0%    10%    20%    30%    40%    50%    60%    70%    80%    90%   100% 
##    5.0    6.0    8.0   10.0   14.0   19.0   29.0   46.0   80.8  183.0 1966.0
for(k1 in names(pathways)){
  p1 = pathways[[k1]]
  pathways[[k1]] = p1[sapply(p1, length) %in% 10:500]
}

Conduct enrichment analysis

dim(gene_info)
## [1] 2000    3
gene_info[1:2,]
##    sym_in_data sym_limma gene_symbol
## 1:        CD38      CD38        CD38
## 2:     PRKAR2B   PRKAR2B     PRKAR2B
gene_dat = fread(sprintf("data/%s_genes_info.csv", cell_type_name))
dim(gene_dat)
## [1] 36517     9
gene_dat[1:2,]
##           gene_ids feature_is_filtered feature_name feature_reference
## 1: ENSG00000000003               FALSE       TSPAN6    NCBITaxon:9606
## 2: ENSG00000000005               FALSE         TNMD    NCBITaxon:9606
##    feature_biotype n_cells_by_counts mean_counts pct_dropout_by_counts
## 1:            gene              6900 0.118699020              90.14412
## 2:            gene               161 0.002485395              99.77003
##    total_counts
## 1:         8310
## 2:          174
length(unique(gene_info$sym_in_data))
## [1] 2000
table(gene_info$sym_in_data %in% gene_dat$feature_name)
## 
## TRUE 
## 2000
table(gene_dat$feature_name %in% gene_info$sym_in_data)
## 
## FALSE  TRUE 
## 34517  2000
gene_dat$selected = 0
gene_dat$selected[match(gene_info$sym_in_data, gene_dat$feature_name)] = 1

table(gene_dat$selected)
## 
##     0     1 
## 34517  2000
tapply(gene_dat$pct_dropout_by_counts, gene_dat$selected, summary)
## $`0`
##      Min.   1st Qu.    Median      Mean   3rd Qu.      Max. 
##   0.00857  90.44551  99.20296  90.72478  99.93429 100.00000 
## 
## $`1`
##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
##    0.00   60.04   81.87   72.81   92.88   97.99
gene_info = merge(gene_info, gene_dat, by.x="sym_in_data", 
                  by.y="feature_name", all.x = TRUE, all.y = FALSE)
dim(gene_info)
## [1] 2000   12
gene_info[1:2,]
##    sym_in_data sym_limma gene_symbol        gene_ids feature_is_filtered
## 1:         A2M       A2M         A2M ENSG00000175899               FALSE
## 2:   A2ML1-AS1 A2ML1-AS1   A2ML1-AS1 ENSG00000256661               FALSE
##    feature_reference feature_biotype n_cells_by_counts mean_counts
## 1:    NCBITaxon:9606            gene              5826   0.1207987
## 2:    NCBITaxon:9606            gene             11030   0.2138297
##    pct_dropout_by_counts total_counts selected
## 1:              91.67821         8457        1
## 2:              84.24488        14970        1
max_n2kp = 10

goseq_res = NULL

for(k in 1:length(gene_sets)){
  if(length(gene_sets[[k]]) < 10) { next }
  
  print(k)
  set_k = paste0("set_", k)
  print(gene_sets[[k]])
  
  genes = gene_info$sym_in_data %in% gene_sets[[k]]
  names(genes) = gene_info$gene_symbol
  table(genes)
  
  pwf = nullp(genes, "hg38", "geneSymbol", 
              bias.data = 100 - gene_info$pct_dropout_by_counts)
  
  for(k1 in names(pathways)){
    p1 = pathways[[k1]]
    res1 = goseq(pwf, "hg38", "geneSymbol", 
                 gene2cat=goseq:::reversemapping(p1))
    res1$FDR  = p.adjust(res1$over_represented_pvalue, method="BH")
    
    nD = sum(res1$FDR < 0.05)
    
    if(nD > 0){
      res1 = res1[order(res1$FDR),][1:min(nD, max_n2kp),]
      res1$category = gsub("REACTOME_|GOBP_", "", res1$category)
      res1$category = gsub("_", " ", res1$category)
      res1$category = tolower(res1$category)
      res1$category = substr(res1$category, start=1, stop=81)
      goseq_res[[set_k]][[k1]] = res1
    }
  }
}
## [1] 1
##  [1] "ARHGAP44" "AMPH"     "PLS3"     "GABRE"    "SH3D19"   "WIPF1"   
##  [7] "RGS4"     "UNC13A"   "RFC3"     "EPHB2"    "BTBD11"   "ABTB2"   
## [13] "PCBP3"    "STAC3"    "ERC2"     "IL1RAPL2" "ITGA3"    "SYN1"    
## [19] "TCOF1"    "TRHDE"    "RIMS1"    "CDKL1"    "CELF4"    "PPFIBP1" 
## [25] "KHDRBS2"  "FGF12"    "RIMS3"    "KIAA1217" "BIN1"     "SRRM4"   
## [31] "ZNF385B"  "ANK3"     "SPTBN4"   "EDIL3"    "ZMAT4"    "GRM5"    
## [37] "REPS2"    "NABP1"    "RIMS2"    "KCNQ5"    "VSTM2B"   "PTPRT"   
## [43] "PARVA"

## [1] 2
##  [1] "SEMA3A"        "TMEM241"       "ALCAM"         "THSD4"        
##  [5] "HLA-E"         "DIO2"          "RNF212B"       "RP1-292B18.4" 
##  [9] "RP1-15D23.2"   "RP4-660H19.1"  "CCDC192"       "LINC00326"    
## [13] "GRM3-AS1"      "LINC02250"     "RBMS3-AS3"     "RP11-475C16.2"
## [17] "RP11-657O9.1"  "RP11-115N4.1"  "MEF2C-AS2"     "ZFPM2-AS1"    
## [21] "LINC00923"     "RP11-116O11.1" "LRRC24"        "RP11-260G13.1"
## [25] "RP11-370I10.2" "DIO2-AS1"      "TSIX"          "SEMA3C"       
## [29] "MAN1A1"        "UST"           "PAM"           "ARID5B"       
## [33] "ZNF385D"       "MGAT5"         "SEMA3D"        "PLCL2"        
## [37] "ART3"          "ELAPOR2"       "PPM1E"         "SAMD12"       
## [41] "RP11-191L9.4"  "TSBP1-AS1"     "RP1-35C21.2"   "LINC01414"

## [1] 3
##  [1] "DNAH9"        "MAOB"         "TACR1"        "LEPR"         "COL4A2"      
##  [6] "LYPD6B"       "IGFBP7"       "METTL2B"      "AGBL2"        "DPP10"       
## [11] "CP"           "ATP9A"        "SPAG1"        "AGFG2"        "ABCC3"       
## [16] "ST8SIA1"      "SERPINI2"     "PRRX1"        "KLHL29"       "MOB3B"       
## [21] "PLXDC2"       "COL21A1"      "HIVEP3"       "PLCE1"        "ENSA"        
## [26] "KCNN3"        "GRIK4"        "ABR"          "DHRS3"        "LRRC2"       
## [31] "ZNF704"       "WNK2"         "GNG4"         "IFFO2"        "NPAS2"       
## [36] "PHYHD1"       "APOLD1"       "TSHZ2"        "ZBTB7C"       "RILPL1"      
## [41] "TRPV1"        "ZNF594-DT"    "RP11-93B21.2"

## [1] 4
##  [1] "GDAP1L1"       "MT1G"          "AGBL3"         "HHIP"         
##  [5] "CLMP"          "MT1E"          "MFSD4B"        "SGCZ"         
##  [9] "FSIP2"         "ANKUB1"        "RP11-131L23.1" "TMLHE-AS1"    
## [13] "ST7-AS2"       "SNAP25-AS1"    "Z83001.1"      "PCDH9-AS2"    
## [17] "AC009501.4"    "GNG12-AS1"     "LINC00513"     "LINC01877"    
## [21] "RP5-1101C3.1"  "PTPRG-AS1"     "ZBTB20-AS5"    "RORA-AS1"     
## [25] "C1QTNF7-AS1"   "RP11-223C24.1" "LINC01618"     "RP11-517I3.1" 
## [29] "CTD-3239E11.2" "RP11-649G15.2" "MPPED2-AS1"    "BBOX1-AS1"    
## [33] "CTD-2537O9.1"  "RP11-315E17.1" "LINC01579"     "RP11-184D12.1"
## [37] "LINC01572"     "PRKCA-AS1"     "LINC02664"     "CH17-140K24.2"
## [41] "RP11-470M1.2"  "RP11-589M4.5"  "RP11-221G19.1" "RP11-555K12.4"
## [45] "DISP3"

## [1] 5
##  [1] "HHAT"           "PEX5L"          "DNAH6"          "PEBP4"         
##  [5] "EFCAB11"        "MLIP"           "SPATA17"        "STPG2"         
##  [9] "ODAD2"          "DNAH12"         "RFLNA"          "WDR97"         
## [13] "ENO4"           "PIWIL2"         "HMGN5"          "CRPPA"         
## [17] "LGALSL-DT"      "CHL1-AS2"       "LINC01876"      "AC105760.2"    
## [21] "LINC01185"      "AC008269.2"     "PATL2"          "RPL34-DT"      
## [25] "LINC01524"      "DRAIC"          "CTB-161M19.4"   "LINC01182"     
## [29] "CTC-347C20.1"   "CTB-178M22.2"   "RP11-727A23.10" "RP11-511B23.2" 
## [33] "RP11-352M15.1"  "SPESP1"         "RP11-525K10.3"  "RP11-396B14.2" 
## [37] "RP11-397A16.1"  "LINC00506"      "RP5-847G17.1"   "RP11-444C24.1" 
## [41] "RP11-96C13.1"   "RP11-520F22.1"  "DNAH5"          "AC104088.1"

## [1] 6
##  [1] "PON3"          "TENT5A"        "MTERF1"        "PKIB"         
##  [5] "SCN11A"        "CATSPERE"      "LINC01006"     "GPR39"        
##  [9] "COL25A1"       "CC2D2B"        "RP11-306O13.1" "COL28A1"      
## [13] "AC026188.1"    "POT1-AS1"      "PLCG1-AS1"     "AC012593.1"   
## [17] "SOX21-AS1"     "LYPLAL1-DT"    "LNC-LBCS"      "HDAC2-AS2"    
## [21] "LINC01277"     "LINC01937"     "LINC01239"     "PPP1R9A-AS1"  
## [25] "AC079305.11"   "RP11-4B14.3"   "NECTIN3-AS1"   "RP11-167H9.4" 
## [29] "RP11-436F23.1" "LINC02196"     "RP11-404I7.2"  "LINC00534"    
## [33] "RP11-804N13.1" "RMST"          "PRANCR"        "RP11-72M17.1" 
## [37] "AC004158.3"    "CTC-498M16.4"  "RP11-69G16.2"  "RP4-660H19.2" 
## [41] "RP3-383B8.1"   "RP11-346I3.7"  "RP1-84D21.2"   "RP11-120J1.2" 
## [45] "RP11-168F16.1"

## [1] 7
##  [1] "MRC2"      "ABCC2"     "IDI1"      "RIPK2"     "EPM2A"     "HES1"     
##  [7] "PPP1R3C"   "BCL2L14"   "EEPD1"     "MT2A"      "ID1"       "IFI6"     
## [13] "APOE"      "CCDC59"    "GULP1"     "CCDC102B"  "SETBP1"    "GRIA4"    
## [19] "LMOD1"     "SYNPR"     "HNF4G"     "PAPPA"     "CALN1"     "KCTD16"   
## [25] "CCSER1"    "PDXP"      "ARHGAP8"   "MRPL33"    "TLE2"      "KNOP1"    
## [31] "FSD1"      "USP9Y"     "PDE1A"     "ARID3A"    "DOCK10"    "MCPH1"    
## [37] "NLGN4Y"    "CKB"       "NXNL1"     "TTTY14"    "UTY"       "MITF"     
## [43] "LINC00278"

## [1] 8
##  [1] "BID"      "GAB2"     "SDK2"     "BLVRB"    "SLC39A14" "GMDS"    
##  [7] "SIPA1L2"  "PRR5L"    "CADPS"    "HPRT1"    "SNTB1"    "GLRX"    
## [13] "HEG1"     "ROBO2"    "MALAT1"   "CD99"     "GAS7"     "VRK2"    
## [19] "DOK5"     "COTL1"    "BNIP3L"   "SIPA1L3"  "ZMIZ1"    "GAB1"    
## [25] "TANC1"    "ECE1"     "TSHZ3"    "ZFP36"    "RFTN1"    "TNS3"    
## [31] "GABPB2"   "DIAPH2"   "ZEB1"     "DGKZ"     "ADCY9"    "EVA1C"   
## [37] "IRS1"     "BCL2"     "ANO6"     "SYN3"     "IRS2"     "PLCG2"   
## [43] "CPEB1"

## [1] 9
##  [1] "SLC26A8"       "WDR64"         "LINC01931"     "GLIPR1L1"     
##  [5] "P2RY14"        "HEPN1"         "AC002463.3"    "RP11-547I7.1" 
##  [9] "AC017101.10"   "RP11-141A19.1" "RP11-417B4.2"  "GNA14-AS1"    
## [13] "RP11-46O21.2"  "GPC5-AS2"      "AC037445.1"    "PCDH9-AS4"    
## [17] "RP11-666F17.1" "RP11-109I13.2" "STARD13-AS"    "GS1-433O24.1" 
## [21] "AC008067.2"    "RP13-143G15.4" "LINC00960"     "RP11-768G7.3" 
## [25] "GK-AS1"        "LRP4-AS1"      "ANK2-AS1"      "MAPK10-AS1"   
## [29] "RP11-120A1.1"  "RP11-39E3.3"   "STPG2-AS1"     "RP11-351A11.1"
## [33] "RP11-463D19.1" "AP000462.2"    "RP11-513G19.1" "A2ML1-AS1"    
## [37] "RP11-39M21.1"  "CRIM1-DT"      "RP11-58G13.1"  "AC005786.7"   
## [41] "RP11-138H11.1" "CTD-2282P23.2" "RP11-576O3.1"  "RP11-394G3.3" 
## [45] "RP11-66G15.1"

## [1] 10
##  [1] "APBA1"    "DHRS7B"   "FAXC"     "ABHD3"    "ARHGAP31" "APBA2"   
##  [7] "RRP12"    "DGKG"     "CDON"     "PFKP"     "PHACTR3"  "MYO9B"   
## [13] "PALM"     "CAB39L"   "EEF2K"    "SYT17"    "OLFM2"    "COBL"    
## [19] "LIN7A"    "CCND3"    "TFDP2"    "FOXO3"    "HIF3A"    "HIP1"    
## [25] "RIN2"     "MAPK4"    "NFIC"     "BOC"      "ARHGAP26" "TIAM2"   
## [31] "FAM171A1" "FOXO1"    "C2CD2"    "AHCYL2"   "EPB41"    "FBXO27"  
## [37] "ZFPM2"    "FAM222B"  "PACS1"    "CADM1"    "ANKS1B"   "DMWD"    
## [43] "DACH1"

## [1] 11
##  [1] "PNPLA3"   "GALNT16"  "ELAVL2"   "SLC2A9"   "PPM1H"    "ACAT2"   
##  [7] "PTH1R"    "PBX3"     "TMEM51"   "CERS6"    "CES2"     "SMYD3"   
## [13] "PCLO"     "PDE4A"    "RASAL2"   "PIR"      "CERS4"    "MAST3"   
## [19] "PLIN3"    "UBE2R2"   "SH3PXD2A" "LRRC4B"   "SLC39A11" "NAV1"    
## [25] "SSH2"     "ITPKB"    "SNTG1"    "CACNA1B"  "FSIP1"    "MAGI1"   
## [31] "AKAP6"    "CLSTN2"   "PKNOX2"   "PLEKHA7"  "LDLRAD4"  "PTPN9"   
## [37] "CMTM4"    "RALYL"    "ELAVL3"   "RYR2"     "PCAT1"

## [1] 12
##  [1] "PCSK1N"         "SRPX2"          "POLR2I"         "LRRC9"         
##  [5] "H3-3B"          "CA1"            "ITGA9"          "LRTM1"         
##  [9] "CHST9"          "SHOC1"          "FILIP1L"        "DLEU1"         
## [13] "TSBP1"          "MT1H"           "AC105461.1"     "ASTN2-AS1"     
## [17] "RP4-613B23.1"   "DPP10-AS3"      "IPO9-AS1"       "DPP10-AS1"     
## [21] "LINC02877"      "PRKAR2B-AS1"    "RP11-274H2.2"   "BAALC-AS1"     
## [25] "CTD-2015H6.3"   "RP11-711G10.1"  "RP11-452H21.1"  "AP000487.6"    
## [29] "RP11-1H15.2"    "RP11-867G2.8"   "RP11-144F15.1"  "RP11-887P2.5"  
## [33] "RP11-363J20.2"  "HIF1A-AS3"      "CTC-513N18.6"   "RP11-355F16.1" 
## [37] "RP11-80I3.1"    "SLC7A14-AS1"    "RP11-793H13.14" "CTD-2172F7.1"  
## [41] "RP11-725F23.1"  "RP11-875G18.1"  "NUP210L"        "SMOC1"         
## [45] "TTTY10"

## [1] 13
##  [1] "CD38"          "CALCRL"        "SIDT1"         "CCDC80"       
##  [5] "IFI44L"        "SLC24A4"       "SAXO1"         "PKD1L1"       
##  [9] "CD200R1"       "ADAMTS9"       "GUCY1A1"       "KIF6"         
## [13] "FREM1"         "VWA3B"         "NRG4"          "DELEC1"       
## [17] "VWA3A"         "SCOC-AS1"      "STUM"          "RP11-735G4.1" 
## [21] "LINC01515"     "RP11-106M7.1"  "DIRC3"         "DIRC3-AS1"    
## [25] "LINC01695"     "AC007563.5"    "RP11-132E11.2" "RP11-624M8.1" 
## [29] "RP11-114J13.1" "NEUROG2-AS1"   "VCAN-AS1"      "RP11-669M16.1"
## [33] "LINC02715"     "RP11-708B6.2"  "MAP1LC3B2"     "FRMD6-AS2"    
## [37] "PTCSC3"        "RP11-323P17.2" "RP11-290O12.2" "CTC-490G23.6" 
## [41] "RP11-274G22.1" "RP11-364P22.4" "RP11-373E16.6" "CTD-2040G12.2"
## [45] "RP11-423B13.1"

## [1] 14
##  [1] "XK"            "CTD-2313D3.2"  "FAP"           "SLCO1A2"      
##  [5] "LAMB4"         "CATSPERG"      "CACNA1I"       "DNAH11"       
##  [9] "TGIF2"         "AK7"           "CCDC3"         "GAL3ST2"      
## [13] "TDRD9"         "DRC1"          "CFAP251"       "SHROOM4"      
## [17] "ZNF653"        "ARMC3"         "PPP1R36"       "PDZRN4"       
## [21] "C2"            "TVP23A"        "TEKT1"         "ATOH8"        
## [25] "GSG1L"         "NOTUM"         "C7orf61"       "CFAP54"       
## [29] "ODAD4"         "LINC01208"     "NRSN2-AS1"     "AC092155.4"   
## [33] "ARL17B"        "HMGA1P4"       "RP5-827C21.2"  "KCNK15-AS1"   
## [37] "CTB-35F21.1"   "RP11-279O9.4"  "LINC02315"     "LINC02356"    
## [41] "RP11-876N24.2" "CTD-2189E23.1" "SPANXA2-OT1"   "RP11-301F14.1"
## [45] "CTD-2201E18.6"

## [1] 15
##  [1] "CDH10"   "PRKCQ"   "MBNL3"   "EPHA6"   "TRPM3"   "MT3"     "CEMIP"  
##  [8] "SCG3"    "SLC1A2"  "EPHA4"   "AKAP12"  "EMP1"    "CD72"    "ABCA12" 
## [15] "TMEM108" "CXCL14"  "ACSL1"   "WIF1"    "GALNT10" "DLC1"    "LRRC3B" 
## [22] "EXT1"    "CMSS1"   "KLHL32"  "GCNT1"   "BRINP2"  "ATP1A2"  "MCF2L2" 
## [29] "NGEF"    "PLXNA2"  "SESN1"   "KIF3C"   "STAG1"   "VAV3"    "CPM"    
## [36] "CEP350"  "SHROOM3" "CRADD"   "PCDH7"   "SWI5"    "NCKAP5"  "LSMEM2" 
## [43] "EFNA5"   "S100A10"

## [1] 16
##  [1] "MAP3K7CL"      "LRRIQ3"        "MN1"           "RHCE"         
##  [5] "AC074391.1"    "PPP1R26-AS1"   "EPS15-AS1"     "XIST"         
##  [9] "LINC02884"     "LINC01934"     "LINC00886"     "SUCLG2-AS1"   
## [13] "LINC01301"     "LINC00637"     "RP11-692P14.1" "GRK3"         
## [17] "RIPOR2"        "TFCP2L1"       "DMGDH"         "GMPR"         
## [21] "MRAS"          "VWA5B1"        "RFTN2"         "FAXDC2"       
## [25] "CHST11"        "LDLRAD3"       "NWD1"          "TMEM184B"     
## [29] "PLIN5"         "LINC00598"     "PDYN-AS1"      "ARHGEF26-AS1" 
## [33] "RTL9"          "ALDH1L1-AS2"   "STX18-AS1"     "RP11-150C16.1"
## [37] "RP11-838N2.5"  "AC079610.1"    "RP11-711K1.8"  "RP11-358F13.1"
## [41] "RP1-166D18.1"  "RP11-26L21.1"  "RP11-166M16.1" "RP11-421A16.1"
## [45] "RP11-404C6.6"

## [1] 17
##  [1] "AHRR"           "CPED1"          "WNT5B"          "DNAH7"         
##  [5] "APOC1"          "CABLES1"        "C10orf90"       "AXDND1"        
##  [9] "HOPX"           "TMEM132C"       "CCBE1"          "RFX8"          
## [13] "NPSR1-AS1"      "LINC01117"      "LINC01768"      "CENATAC-DT"    
## [17] "RP11-496B10.6"  "SAMD4A"         "PPP1R15A"       "ISYNA1"        
## [21] "CPEB3"          "TPD52L1"        "C1orf21"        "WLS"           
## [25] "PDZRN3"         "TOX2"           "SLC22A23"       "GLTP"          
## [29] "ADAMTS10"       "SDK1"           "DOC2A"          "PID1"          
## [33] "GNA14"          "ZNF208"         "CACNB2"         "GPR176"        
## [37] "DHRSX"          "GNG7"           "CTD-2527I21.15" "AJAP1"         
## [41] "TOX"            "LINC00511"      "HPN-AS1"

## [1] 18
##  [1] "USH1C"                   "ATP11A"                 
##  [3] "MGAT3"                   "NXN"                    
##  [5] "GTF2IRD1"                "HDAC9"                  
##  [7] "PDZD4"                   "ITPKC"                  
##  [9] "RELB"                    "AEBP1"                  
## [11] "CDH23"                   "WASF1"                  
## [13] "IL1R1"                   "PADI2"                  
## [15] "ZC4H2"                   "QRICH2"                 
## [17] "GALNT8"                  "ZSWIM4"                 
## [19] "PTPRE"                   "TMTC1"                  
## [21] "IRAK2"                   "DENND2A"                
## [23] "DOCK11"                  "RHPN1"                  
## [25] "ORAI2"                   "TMCO4"                  
## [27] "SHISA5"                  "TMC1"                   
## [29] "KIF5C"                   "HAP1"                   
## [31] "SPATA13_ENSG00000182957" "RTN4RL1"                
## [33] "COL27A1"                 "RASGEF1A"               
## [35] "NHSL2"                   "TCEA3"                  
## [37] "S1PR3"                   "MEF2B"                  
## [39] "LINC00685"               "EPCAM-DT"               
## [41] "L3MBTL2-AS1"             "KLF2-DT"                
## [43] "AF038458.3"              "FBXO17"                 
## [45] "DGCR5_ENSG00000273032"

## [1] 19
##  [1] "SEL1L2"        "RERG"          "MAEL"          "SLC22A3"      
##  [5] "ADRA1B"        "PAH"           "SLC24A3"       "NAP1L3"       
##  [9] "CYP4X1"        "DCHS2"         "GRM3"          "MRPS9-AS2"    
## [13] "AP000282.2"    "LINC01344"     "AC007682.1"    "AC009264.1"   
## [17] "RP11-142A5.1"  "RP11-154H17.1" "LINC02234"     "HS3ST5"       
## [21] "F11-AS1"       "RP1-84O15.2"   "RP11-317N12.1" "ZFHX4-AS1"    
## [25] "RP11-541P9.3"  "RP11-431M3.1"  "RP11-134O21.1" "LINC02763"    
## [29] "LINC02327"     "RP11-526N18.1" "RP11-242P2.1"  "PLS3-AS1"     
## [33] "RP11-561I11.4" "LINC00540"     "RP11-378A12.1" "LINC01727"    
## [37] "CH17-174L20.1" "RP11-624A4.2"  "CALCB"         "FZD9"         
## [41] "AC016745.3"    "MEIKIN"        "RP11-328J6.1"  "RP11-237N2.1" 
## [45] "RP11-183J19.1"

## [1] 20
##  [1] "ZFR2"           "MOGAT1"         "PUDP"           "DPH6"          
##  [5] "TMEM132B"       "SLC14A1"        "KIAA1328"       "DNAAF1"        
##  [9] "ERICH3"         "HDHD5-AS1"      "CLDN4"          "FIRRE"         
## [13] "LIPE-AS1"       "FBXO16"         "AC004540.5"     "RP11-162D16.2" 
## [17] "RP11-498J9.2"   "AC079807.4"     "MMADHC-DT"      "RAP2C-AS1"     
## [21] "RP11-120D5.1"   "COX10-AS1"      "RP11-410D17.2"  "RP11-461O7.1"  
## [25] "RP11-373N22.3"  "LINC02144"      "RP11-130F10.1"  "RP11-284M14.1" 
## [29] "RP11-679C8.2"   "MAILR"          "GS1-57L11.1"    "RP11-156K13.1" 
## [33] "RP11-20E24.1"   "RP11-571L19.7"  "RP11-524F11.2"  "CTD-2349P21.11"
## [37] "ADGRL1-AS1"     "GEMIN7-AS1"     "RP11-413N10.3"  "RP11-281A20.2" 
## [41] "RP11-314E10.1"  "RP11-563M4.2"   "TPCN1"          "C3orf35"       
## [45] "AP000318.2"

## [1] 21
##  [1] "NID1"           "ST6GALNAC5"     "F3"             "C2CD6"         
##  [5] "MEGF11"         "OTOGL"          "MACROD2"        "CYP7B1"        
##  [9] "C12orf42"       "TAFA1"          "HES5"           "ADD3-AS1"      
## [13] "LCNL1"          "AP000233.4"     "MIR181A1HG"     "LINC01036"     
## [17] "RP1-45C12.1"    "OBI1-AS1"       "RNF217-AS1"     "LINC02652"     
## [21] "SOX2-OT"        "LINC00504"      "LINC01950"      "RP11-582J16.4" 
## [25] "LINC02389"      "LINC02328"      "RP11-103J8.1"   "RP11-436D23.1" 
## [29] "RP11-57G22.3"   "RP11-437L7.2"   "RP11-1289C17.1" "RP11-399K19.1" 
## [33] "CTD-2297M2.1"   "TENM2"          "SLC5A11"        "LINGO1"        
## [37] "PDE3A"          "GPR137C"        "ZNF804B"        "PLK5"          
## [41] "KBTBD12"        "DLEU2"          "AC002127.4"     "KCNMB2-AS1"    
## [45] "LINC01252"

## [1] 22
##  [1] "SEZ6L"                 "CAP2"                  "TACC2"                
##  [4] "ARHGAP18"              "PLEKHG4B"              "MON1A"                
##  [7] "SLC43A2"               "RAB39A"                "C9orf153"             
## [10] "KIF5C-AS1"             "RP11-390F4.6"          "LINC00877"            
## [13] "TRMT9B"                "CTD-2126E3.6"          "MAP3K9"               
## [16] "PDK3"                  "RASGRP2"               "ADGRL1"               
## [19] "ARHGAP15"              "EBF4"                  "TICAM1"               
## [22] "ZBTB46"                "KIAA0513"              "NKD1"                 
## [25] "CCDC40"                "MVB12A"                "CLVS2"                
## [28] "RIT2"                  "ST3GAL2"               "C1orf87"              
## [31] "FAAH2"                 "PIK3CD"                "VAT1L"                
## [34] "SYT12"                 "PPP1R42"               "LINC00862"            
## [37] "LYRM4"                 "STARD10"               "MTRNR2L1"             
## [40] "RPPH1_ENSG00000259001" "RP11-35G9.5"           "CASTOR2"              
## [43] "RP11-465L10.14"

## [1] 23
##  [1] "LINC01630"               "MTRNR2L8"               
##  [3] "LINC01374"               "USH2A"                  
##  [5] "SLC26A3"                 "STEAP1B"                
##  [7] "KLF2"                    "LGR6"                   
##  [9] "RHBDL3"                  "ESYT3"                  
## [11] "SYTL3"                   "PTCHD1"                 
## [13] "GREM1"                   "SEMA3E"                 
## [15] "MRGPRF"                  "AC023469.1"             
## [17] "AC003090.1"              "AC064875.2"             
## [19] "RP11-563D10.1"           "LINC01320"              
## [21] "RP11-154D17.1"           "AC013463.2"             
## [23] "RP11-305L7.3"            "AC002066.1"             
## [25] "RP11-384F7.1"            "RP11-17A1.3"            
## [27] "LINC02742"               "RP11-79E3.2"            
## [29] "LINC02208"               "LINC01609"              
## [31] "RP11-958J22.1"           "RP11-20D14.3"           
## [33] "RP11-507B12.2"           "RP11-507B12.1"          
## [35] "LINC00558"               "MTRNR2L12"              
## [37] "RMRP_ENSG00000269900"    "SCARNA2_ENSG00000270066"
## [39] "RP11-154H23.4"           "CH507-513H4.1"          
## [41] "CH507-528H12.1"          "RP11-596C23.6"          
## [43] "RP11-379B18.8"           "RP4-799O8.1"            
## [45] "AC003099.2"              "RP11-398J12.1"

## [1] 24
##  [1] "ANOS1"            "MAMLD1"           "KIAA1549L"        "PDE8B"           
##  [5] "TFAP2E"           "KCTD1"            "SLC44A3"          "LIX1"            
##  [9] "DUSP15"           "PCED1B"           "PRELID2"          "SLC4A5"          
## [13] "MAML3"            "SULT1A2"          "MAMDC2-AS1"       "CTA-292E10.6"    
## [17] "RP1-167A14.2"     "RP1-223B1.1"      "LINC01725"        "RP1-230L10.1"    
## [21] "LINC00407"        "LEFTY1"           "OSMR-AS1"         "RP11-1252I4.2"   
## [25] "RP4-785G19.5"     "LINC00958"        "DISC1FP1"         "RP11-574F11.4"   
## [29] "DGKB"             "LRGUK"            "DEPTOR"           "ADCY1"           
## [33] "FRMD3"            "TOGARAM2"         "AP001347.6"       "XXbac-BPG55C20.7"
## [37] "RP11-69I8.3"      "CYP1B1-AS1"       "LINC00884"        "AL163953.3"      
## [41] "MIR4300HG"        "LINC01094"        "CTD-2054N24.2"    "RP11-210M15.2"   
## [45] "RP11-114N19.3"

## [1] 25
##  [1] "OSBPL3"       "SYTL4"        "UBE3D"        "BICC1"        "GFRA1"       
##  [6] "SPOCK1"       "C4orf19"      "MMP16"        "RNF150"       "LRRN2"       
## [11] "MTSS1"        "C1QTNF4"      "ZNF497"       "RNLS"         "ROR1"        
## [16] "SHISA6"       "L3MBTL3"      "SAMD13"       "LINC01266"    "AC097721.2"  
## [21] "NPIPB2"       "RP11-11N9.4"  "CTXND1"       "COL23A1"      "SYNE2"       
## [26] "TBC1D1"       "RARB"         "PPARGC1A"     "ARSB"         "CHD5"        
## [31] "PRR12"        "FCHO1"        "THRB"         "FAM107A"      "SLC25A20"    
## [36] "SPACA6"       "PAX8-AS1"     "RP5-921G16.1" "RP11-26J3.1"  "RP11-298I3.1"
## [41] "CASC17"       "AGBL1"        "LINC02246"

## [1] 26
##  [1] "MYO16"        "PPEF1"        "EPB41L4B"     "SGK2"         "NT5DC3"      
##  [6] "FRK"          "MASP1"        "TESPA1"       "GPNMB"        "PLK2"        
## [11] "ARHGAP27"     "CCDC141"      "C4orf45"      "SSR4"         "BAALC-AS2"   
## [16] "CCDC124"      "DCN"          "CDH3"         "ATP2B3"       "CASS4"       
## [21] "SLC7A5"       "ADAP1"        "EPHB6"        "SUSD1"        "DUSP1"       
## [26] "PMEPA1"       "EDA2R"        "SLC6A6"       "HAVCR2"       "MICAL1"      
## [31] "ARHGAP29"     "EGF"          "SLC43A1"      "ITPR1"        "CNKSR3"      
## [36] "FBXO32"       "CATIP"        "ITGA2"        "NT5DC2"       "MOB3A"       
## [41] "MB21D2"       "HAUS7"        "RP11-60A24.3"

## [1] 27
##  [1] "KCNN2"    "IQCH"     "LAMA4"    "DPYSL3"   "ENOX1"    "ABCC4"   
##  [7] "FADS2"    "ARRDC4"   "ST6GAL2"  "ABI3BP"   "NDUFAF2"  "TSPAN5"  
## [13] "GPR156"   "CA8"      "GINS3"    "IMMP2L"   "MGAM"     "SLC7A2"  
## [19] "HSD17B14" "RNF24"    "KAT8"     "PPP1R13L" "B4GALT2"  "DPP6"    
## [25] "NCAN"     "CCNH"     "BCAS3"    "COL6A2"   "CNNM2"    "DPYSL5"  
## [31] "PDPN"     "ABCA1"    "FAT3"     "ENOX2"    "ZNF608"   "PFKFB3"  
## [37] "SLC35E3"  "RGMA"     "ABAT"     "EFCAB2"   "C19orf38" "EML6"

## [1] 28
##  [1] "NTN1"          "IL7"           "GABRA4"        "RPS15"        
##  [5] "HSD11B1"       "RPL36"         "RPLP1"         "PDE5A"        
##  [9] "RNF165"        "FAU"           "ZNF48"         "SEPTIN1"      
## [13] "PLD5"          "KCNB2"         "SP140L"        "MT1X"         
## [17] "EYS"           "KCNMB2"        "RPS18"         "LUCAT1"       
## [21] "RP11-348J24.1" "KCNG1"         "ZFY"           "RHOBTB1"      
## [25] "ANGPT2"        "PCDH11Y"       "KCNN1"         "TSPAN11"      
## [29] "TNNT2"         "NRP2"          "HS3ST2"        "AIF1L"        
## [33] "C1QL1"         "KCNH5"         "PXDNL"         "SPATA2L"      
## [37] "FGF17"         "ST8SIA3"       "POTEG"         "RP11-147G16.1"
## [41] "ETV5"

## [1] 29
##  [1] "TENM1"    "TMSB10"   "EFEMP1"   "BEX1"     "CACNA1A"  "SHANK2"  
##  [7] "VWCE"     "DLGAP2"   "CNTN1"    "RIMBP2"   "CTNNA2"   "SYT1"    
## [13] "RBFOX1"   "TGFB2"    "PCSK5"    "GLIS3"    "CPE"      "CLNK"    
## [19] "MACF1"    "PALLD"    "SOX5"     "ARHGEF4"  "PCSK6"    "ECE2"    
## [25] "NCAM2"    "SHANK1"   "OXR1"     "RBFOX3"   "SLC20A2"  "FRMPD4"  
## [31] "DLGAP1"   "FRMD5"    "CNTNAP2"  "SH3PXD2B" "CSMD1"    "OPCML"   
## [37] "CNTN2"    "DUSP8"    "ZFP36L1"  "KCNIP4"   "ARID5A"   "SRGAP1"  
## [43] "ZNF358"   "NEAT1"

## [1] 30
##  [1] "WSCD2"         "SLC8A3"        "PLCB4"         "CHODL"        
##  [5] "BNC2"          "CYP4F12"       "CYP4F3"        "INSYN2B"      
##  [9] "LINC02814"     "AC092684.1"    "SOCS2-AS1"     "LINC02326"    
## [13] "RP11-116N8.1"  "RP11-104E19.1" "MAPT-AS1"      "RP11-793A3.2" 
## [17] "RP11-354K4.2"  "LINC00836"     "LINC00842"     "RP11-492O8.3" 
## [21] "RP11-259G3.1"  "RP11-154D6.3"  "RP11-609L3.3"  "RP1-20N4.2"   
## [25] "ARHGAP6"       "CCDC175"       "ANGPT1"        "SAMD3"        
## [29] "METTL7B"       "SAMD11"        "LAMA2"         "PLPP4"        
## [33] "RP11-174G6.1"  "RP11-90C4.1"   "LINC01088"     "RP11-346L1.2" 
## [37] "LINC00609"     "LINC02251"     "RP11-259K15.2" "RP11-627D16.1"
## [41] "RP11-499F3.2"  "RP11-114N1.1"  "RP11-542F9.2"  "RP5-1015P16.1"
## [45] "RP11-6L16.1"

## [1] 31
##  [1] "REEP1"    "RASD1"    "ADCY7"    "TRIM5"    "LPAR4"    "FABP5"   
##  [7] "SVEP1"    "SCG5"     "AQP1"     "KLHL13"   "FOSL2"    "GADD45B" 
## [13] "NFATC2"   "IGSF21"   "ID3"      "ITIH5"    "RTN2"     "JUND"    
## [19] "RTN1"     "CREB5"    "ADAM12"   "SEC24D"   "KCNE4"    "RASSF3"  
## [25] "GDPD5"    "ARHGAP35" "ATF3"     "TMEM200A" "NFIL3"    "FOS"     
## [31] "JUNB"     "CXXC5"    "SPSB1"    "PLEKHG5"  "RND1"     "PAWR"    
## [37] "YOD1"     "RGS6"     "FAM110C"  "MAFF"     "TRDN"     "CRYBB2"

## [1] 32
##  [1] "NRXN3"         "PSD"           "BCAS1"         "RPH3A"        
##  [5] "SLC16A6"       "CALY"          "KIRREL3"       "NDST3"        
##  [9] "JAM3"          "GRIK1"         "GALNTL6"       "GRM7"         
## [13] "CARNMT1-AS1"   "RP11-170M17.1" "AC011288.2"    "RP1-232L24.3" 
## [17] "LINC02217"     "C5orf17"       "RP4-809F18.1"  "LINC02254"    
## [21] "PWRN1"         "PRAG1"         "RP11-239A17.1" "CTC-428H11.2" 
## [25] "RP11-125D12.3" "RP11-320L2.1"  "BAIAP3"        "P2RX7"        
## [29] "SEC14L5"       "ATRNL1"        "SCN2A"         "SLC4A10"      
## [33] "ST18"          "CNTN5"         "NLGN1"         "SLC8A1"       
## [37] "PDE2A"         "CCK"           "SHTN1"         "CACNA1E"      
## [41] "MMP17"         "MEG3"          "RP1-30E17.2"   "RP11-190P13.2"
## [45] "IQCJ-SCHIP1"

## [1] 33
##  [1] "ARHGAP28"     "PHACTR2"      "ELL2"         "FHAD1"        "RNF175"      
##  [6] "HS3ST3A1"     "RETREG1"      "GFRA2"        "STK32A"       "SNX31"       
## [11] "RP11-364L4.3" "APP-DT"       "RP5-965G21.3" "ST6GALNAC2"   "ST6GAL1"     
## [16] "P3H2"         "CLIP2"        "JHY"          "MAN1C1"       "LRAT"        
## [21] "TTC9"         "SCN1A"        "PARP8"        "NFASC"        "ARHGEF3"     
## [26] "CFAP47"       "SLITRK5"      "TPST1"        "COL24A1"      "RCAN2"       
## [31] "PRIMA1"       "CAVIN1"       "PLCXD3"       "CHST6"        "OVCH1"       
## [36] "LINC00632"    "CFI"          "RP1-111D6.3"  "SATB1-AS1"    "CTD-2643I7.5"
## [41] "LINC01411"    "LINC02506"    "RP1-79C4.4"   "RP11-403A3.3" "RP11-403A3.2"

## [1] 34
##  [1] "LRRC7"         "SNCAIP"        "SP140"         "STS"          
##  [5] "ANKRD7"        "B3GAT2"        "PLAGL1"        "GTDC1"        
##  [9] "UNC79"         "ARSG"          "SUMF1"         "BEND6"        
## [13] "SYCP2L"        "GRIK2"         "ALDH1A1"       "PRTG"         
## [17] "ANO5"          "NEGR1"         "RGS7"          "PNMA3"        
## [21] "KIAA0825"      "LINC02649"     "LINC00571"     "AC072062.3"   
## [25] "SNHG31"        "RP11-154D6.1"  "PKN2-AS1"      "RP11-446H18.5"
## [29] "CXXC4-AS1"     "SEMA6A-AS1"    "RP11-673E1.1"  "RP11-586K2.1" 
## [33] "AB015752.3"    "RP11-624D11.2" "RP11-798K3.2"  "CRTC3-AS1"    
## [37] "LINC00907"     "ARRDC3-AS1"    "RP4-681L3.3"   "RP11-592G13.2"
## [41] "RP11-335E8.3"  "RNF19A"        "ZMAT3"         "RP3-466I7.2"

## [1] 35
##  [1] "MAP2K6"       "PDE10A"       "GBE1"         "PSG8"         "HS3ST3B1"    
##  [6] "EPSTI1"       "ANKRD33B"     "FSTL5"        "SGCD"         "SLIT1"       
## [11] "TENM3"        "SOX1-OT"      "AC007193.6"   "HGF"          "COL5A3"      
## [16] "WFDC1"        "XYLT1"        "NAMPT"        "UNC5B"        "SPP1"        
## [21] "CCND2"        "LOXL1"        "PTPRJ"        "FREM2"        "KCNJ16"      
## [26] "PTMS"         "ADORA1"       "RANBP3L"      "MAP1A"        "LRRC8C"      
## [31] "CSDC2"        "HPSE2"        "ARPP21"       "FZD8"         "NME9"        
## [36] "PCP4"         "ZNF98"        "DNM3"         "AC003991.3"   "SPRY4-AS1"   
## [41] "LINC01619"    "CEACAM16-AS1" "PKD1L3"

## [1] 36
##  [1] "FAR2"          "FAM117B"       "HMGA2"         "UNC5D"        
##  [5] "TMEM130"       "ZCCHC18"       "EPHX4"         "STOX2"        
##  [9] "RNF212"        "WNT7B"         "RANBP17"       "LINC01829"    
## [13] "LINC00499"     "RP11-745L13.2" "RP11-20I20.2"  "RP11-313M3.2" 
## [17] "RP11-175O15.1" "NIPAL3"        "ABCA7"         "CDH20"        
## [21] "TUSC3"         "ARHGEF18"      "LGI1"          "CHRNE"        
## [25] "SEM1"          "ZSWIM6"        "RAP1GAP2"      "ADGRB3"       
## [29] "SLC44A5"       "ABCB9"         "JAZF1"         "IQCK"         
## [33] "CADM2"         "FIGN"          "SLC25A18"      "LHFPL6"       
## [37] "MAML2"         "OSBP2"         "FLRT2"         "NKAIN2"       
## [41] "KIF9-AS1"      "PTCHD1-AS"     "OLMALINC"      "TMEM161B-AS1"

## [1] 37
##  [1] "UPP2"          "PAPPA2"        "RGS22"         "SLC9B1"       
##  [5] "C11orf65"      "SUGCT"         "ZBTB44-DT"     "CASC2"        
##  [9] "LEKR1"         "COL5A2"        "AC007277.3"    "RP11-344B5.2" 
## [13] "TARID"         "ZRANB2-AS2"    "LINC00271"     "RFX3-AS1"     
## [17] "AF131217.1"    "UFL1-AS1"      "RP11-195C7.1"  "LINC01376"    
## [21] "LINC01358"     "CDKN2B-AS1"    "RP11-550I24.2" "H2AZ1-DT"     
## [25] "LINC02355"     "RP11-268P4.5"  "LINC01340"     "LINC02615"    
## [29] "LIX1-AS1"      "C8orf37-AS1"   "LINC02740"     "LINC02745"    
## [33] "RP11-266O8.1"  "LINC02320"     "RP11-111A21.1" "RP11-16B13.1" 
## [37] "RP11-739G5.1"  "PSMD7-DT"      "RP11-157E16.1" "RP11-964E11.3"
## [41] "RP11-341N18.1" "RP11-788A4.3"  "RP5-892C22.1"  "RP11-215I16.3"
## [45] "RP11-446J8.1"

## [1] 38
##  [1] "ANKRD24"       "MROH8"         "SPATA6L"       "TEX9"         
##  [5] "ADAP2"         "MALRD1"        "APTR"          "AP001628.6"   
##  [9] "LMCD1-AS1"     "CTC-329D1.2"   "IDH2-DT"       "SYNPO2L-AS1"  
## [13] "RP11-382N13.7" "TMEM38A"       "RFX2"          "DAAM1"        
## [17] "RFX4"          "IQCA1"         "PATJ"          "LRMDA"        
## [21] "TBX6"          "FAM151B"       "ADCY8"         "NRG2"         
## [25] "NAV2"          "FAM174B"       "CCDC30"        "NOL4L"        
## [29] "TMEM229B"      "AC004951.6"    "RP5-864K19.4"  "RP11-348F1.3" 
## [33] "WARS2-AS1"     "LINC00342"     "LINC01137"     "LINC01135"    
## [37] "DPH6-DT"       "RP11-148E17.1" "RP3-414A15.10" "RP1-158P9.2"  
## [41] "TAPT1-AS1"     "ATP6V0D1-DT"   "RP11-514P8.10" "RP11-799O21.2"
## [45] "RP11-125C10.1"

## [1] 39
##  [1] "CHI3L1"        "FHDC1"         "WARS1"         "BTG2"         
##  [5] "HES4"          "IER5L"         "LINC01503"     "MSC-AS1"      
##  [9] "RP11-380P13.1" "BCL6-AS1"      "RP11-640F22.1" "MCUB"         
## [13] "SYT7"          "KLF6"          "TESC"          "KLHL4"        
## [17] "HELB"          "COL5A1"        "UNC13C"        "CBLN2"        
## [21] "CDH18"         "SLC24A2"       "CFAP161"       "COX7A1"       
## [25] "PGM2L1"        "DEPP1"         "HTR1E"         "SLC38A11"     
## [29] "SLC26A5"       "KCNH7"         "TNFRSF25"      "RP11-513I15.6"
## [33] "MIR34AHG"      "RP1-187B23.1"  "KRTAP5-AS1"    "IQCM"         
## [37] "AC067956.1"    "SHISA9"        "CTC-340A15.2"  "LINC01322"    
## [41] "PTCHD4"        "LINC02223"     "RP11-624C23.1" "MIR23AHG"     
## [45] "RP11-4D11.1"

## [1] 40
##  [1] "RRAGD"         "FAM107B"       "SRPX"          "CLIC5"        
##  [5] "CRISPLD1"      "TRIM22"        "PLXNC1"        "CA3"          
##  [9] "CIITA"         "PROS1"         "F5"            "CCDC26"       
## [13] "RP11-157I4.4"  "RP11-124B13.1" "RP1-41C23.1"   "RP11-255O19.2"
## [17] "AC006296.4"    "VCAN"          "KITLG"         "FRY"          
## [21] "RASL12"        "CCL2"          "SOHLH2"        "ACVR1C"       
## [25] "BEST3"         "GFPT2"         "HNMT"          "LMNTD1"       
## [29] "FBN1"          "NPNT"          "CLIC4"         "SLCO3A1"      
## [33] "NHS"           "DPYD"          "OSTN"          "SLC6A9"       
## [37] "HRAT92"        "LINC02869"     "RP5-1198O20.4" "RP11-469A15.2"
## [41] "RP11-146I2.1"  "MAFG-DT"       "RP3-365E2.1"   "RP11-103P4.1"

for(n1 in names(goseq_res)){
  k = as.numeric(gsub("set_", "", n1))
  print(n1)
  print(gene_sets[[k]])
  print(goseq_res[[n1]])

}
## [1] "set_1"
##  [1] "ARHGAP44" "AMPH"     "PLS3"     "GABRE"    "SH3D19"   "WIPF1"   
##  [7] "RGS4"     "UNC13A"   "RFC3"     "EPHB2"    "BTBD11"   "ABTB2"   
## [13] "PCBP3"    "STAC3"    "ERC2"     "IL1RAPL2" "ITGA3"    "SYN1"    
## [19] "TCOF1"    "TRHDE"    "RIMS1"    "CDKL1"    "CELF4"    "PPFIBP1" 
## [25] "KHDRBS2"  "FGF12"    "RIMS3"    "KIAA1217" "BIN1"     "SRRM4"   
## [31] "ZNF385B"  "ANK3"     "SPTBN4"   "EDIL3"    "ZMAT4"    "GRM5"    
## [37] "REPS2"    "NABP1"    "RIMS2"    "KCNQ5"    "VSTM2B"   "PTPRT"   
## [43] "PARVA"   
## $go_bp
##                                                  category
## 4455                vesicle mediated transport in synapse
## 3465                     regulation of membrane potential
## 4266                          synaptic vesicle exocytosis
## 3767            regulation of synaptic vesicle exocytosis
## 4255                                 synapse organization
## 270  calcium ion regulated exocytosis of neurotransmitter
##      over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 4455            3.045721e-06                0.9999998          8       29
## 3465            8.256041e-06                0.9999989         11       69
## 4266            1.046634e-05                0.9999995          6       16
## 3767            1.938560e-05                0.9999997          4        6
## 4255            2.778852e-05                0.9999955         12       94
## 270             4.712356e-05                0.9999991          4        7
##             FDR
## 4455 0.01367529
## 3465 0.01566463
## 4266 0.01566463
## 3767 0.02176033
## 4255 0.02495409
## 270  0.03526413
## 
## [1] "set_2"
##  [1] "SEMA3A"        "TMEM241"       "ALCAM"         "THSD4"        
##  [5] "HLA-E"         "DIO2"          "RNF212B"       "RP1-292B18.4" 
##  [9] "RP1-15D23.2"   "RP4-660H19.1"  "CCDC192"       "LINC00326"    
## [13] "GRM3-AS1"      "LINC02250"     "RBMS3-AS3"     "RP11-475C16.2"
## [17] "RP11-657O9.1"  "RP11-115N4.1"  "MEF2C-AS2"     "ZFPM2-AS1"    
## [21] "LINC00923"     "RP11-116O11.1" "LRRC24"        "RP11-260G13.1"
## [25] "RP11-370I10.2" "DIO2-AS1"      "TSIX"          "SEMA3C"       
## [29] "MAN1A1"        "UST"           "PAM"           "ARID5B"       
## [33] "ZNF385D"       "MGAT5"         "SEMA3D"        "PLCL2"        
## [37] "ART3"          "ELAPOR2"       "PPM1E"         "SAMD12"       
## [41] "RP11-191L9.4"  "TSBP1-AS1"     "RP1-35C21.2"   "LINC01414"    
## $go_bp
##                                                                category
## 2073 neuron projection extension involved in neuron projection guidance
##      over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 2073            3.398257e-06                        1          4        8
##             FDR
## 2073 0.01525818
## 
## [1] "set_8"
##  [1] "BID"      "GAB2"     "SDK2"     "BLVRB"    "SLC39A14" "GMDS"    
##  [7] "SIPA1L2"  "PRR5L"    "CADPS"    "HPRT1"    "SNTB1"    "GLRX"    
## [13] "HEG1"     "ROBO2"    "MALAT1"   "CD99"     "GAS7"     "VRK2"    
## [19] "DOK5"     "COTL1"    "BNIP3L"   "SIPA1L3"  "ZMIZ1"    "GAB1"    
## [25] "TANC1"    "ECE1"     "TSHZ3"    "ZFP36"    "RFTN1"    "TNS3"    
## [31] "GABPB2"   "DIAPH2"   "ZEB1"     "DGKZ"     "ADCY9"    "EVA1C"   
## [37] "IRS1"     "BCL2"     "ANO6"     "SYN3"     "IRS2"     "PLCG2"   
## [43] "CPEB1"   
## $reactome
##                                                            category
## 484                                         irs mediated signalling
## 959 signaling by type 1 insulin like growth factor 1 receptor igf1r
## 439                             insulin receptor signalling cascade
## 814                                                   ret signaling
## 931                                   signaling by insulin receptor
##     over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 484            4.079403e-05                0.9999994          4        6
## 959            4.079403e-05                0.9999994          4        6
## 439            5.888195e-05                0.9999988          4        7
## 814            1.006975e-04                0.9999973          4        8
## 931            1.316387e-04                0.9999962          4        8
##            FDR
## 484 0.02204148
## 959 0.02204148
## 439 0.02204148
## 814 0.02827083
## 931 0.02956606
## 
## [1] "set_14"
##  [1] "XK"            "CTD-2313D3.2"  "FAP"           "SLCO1A2"      
##  [5] "LAMB4"         "CATSPERG"      "CACNA1I"       "DNAH11"       
##  [9] "TGIF2"         "AK7"           "CCDC3"         "GAL3ST2"      
## [13] "TDRD9"         "DRC1"          "CFAP251"       "SHROOM4"      
## [17] "ZNF653"        "ARMC3"         "PPP1R36"       "PDZRN4"       
## [21] "C2"            "TVP23A"        "TEKT1"         "ATOH8"        
## [25] "GSG1L"         "NOTUM"         "C7orf61"       "CFAP54"       
## [29] "ODAD4"         "LINC01208"     "NRSN2-AS1"     "AC092155.4"   
## [33] "ARL17B"        "HMGA1P4"       "RP5-827C21.2"  "KCNK15-AS1"   
## [37] "CTB-35F21.1"   "RP11-279O9.4"  "LINC02315"     "LINC02356"    
## [41] "RP11-876N24.2" "CTD-2189E23.1" "SPANXA2-OT1"   "RP11-301F14.1"
## [45] "CTD-2201E18.6"
## $go_bp
##            category over_represented_pvalue under_represented_pvalue numDEInCat
## 559 cilium movement            7.610914e-06                0.9999997          6
##     numInCat      FDR
## 559       23 0.034173
## 
## [1] "set_28"
##  [1] "NTN1"          "IL7"           "GABRA4"        "RPS15"        
##  [5] "HSD11B1"       "RPL36"         "RPLP1"         "PDE5A"        
##  [9] "RNF165"        "FAU"           "ZNF48"         "SEPTIN1"      
## [13] "PLD5"          "KCNB2"         "SP140L"        "MT1X"         
## [17] "EYS"           "KCNMB2"        "RPS18"         "LUCAT1"       
## [21] "RP11-348J24.1" "KCNG1"         "ZFY"           "RHOBTB1"      
## [25] "ANGPT2"        "PCDH11Y"       "KCNN1"         "TSPAN11"      
## [29] "TNNT2"         "NRP2"          "HS3ST2"        "AIF1L"        
## [33] "C1QL1"         "KCNH5"         "PXDNL"         "SPATA2L"      
## [37] "FGF17"         "ST8SIA3"       "POTEG"         "RP11-147G16.1"
## [41] "ETV5"         
## $reactome
##                                                        category
## 287                           eukaryotic translation elongation
## 288                           eukaryotic translation initiation
## 610                                 nonsense mediated decay nmd
## 954                                 signaling by robo receptors
## 856                                             rrna processing
## 878                                 selenoamino acid metabolism
## 810           response of eif2ak4 gcn2 to amino acid deficiency
## 429                                         influenza infection
## 975 srp dependent cotranslational protein targeting to membrane
## 705                                          potassium channels
##     over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 287            4.308317e-06                0.9999999          5        9
## 288            4.308317e-06                0.9999999          5        9
## 610            4.308317e-06                0.9999999          5        9
## 954            5.811522e-06                0.9999998          6       19
## 856            6.249210e-06                0.9999999          5       10
## 878            8.788572e-06                0.9999998          5       10
## 810            9.767675e-06                0.9999998          5       10
## 429            1.198253e-05                0.9999997          5       11
## 975            1.565069e-05                0.9999995          5       11
## 705            2.033836e-05                0.9999993          5       13
##             FDR
## 287 0.001403572
## 288 0.001403572
## 610 0.001403572
## 954 0.001403572
## 856 0.001403572
## 878 0.001567014
## 810 0.001567014
## 429 0.001682047
## 975 0.001952858
## 705 0.002162590
## 
## $go_bp
##                    category over_represented_pvalue under_represented_pvalue
## 618 cytoplasmic translation             1.02996e-05                0.9999997
##     numDEInCat numInCat       FDR
## 618          5       12 0.0462452
## 
## [1] "set_34"
##  [1] "LRRC7"         "SNCAIP"        "SP140"         "STS"          
##  [5] "ANKRD7"        "B3GAT2"        "PLAGL1"        "GTDC1"        
##  [9] "UNC79"         "ARSG"          "SUMF1"         "BEND6"        
## [13] "SYCP2L"        "GRIK2"         "ALDH1A1"       "PRTG"         
## [17] "ANO5"          "NEGR1"         "RGS7"          "PNMA3"        
## [21] "KIAA0825"      "LINC02649"     "LINC00571"     "AC072062.3"   
## [25] "SNHG31"        "RP11-154D6.1"  "PKN2-AS1"      "RP11-446H18.5"
## [29] "CXXC4-AS1"     "SEMA6A-AS1"    "RP11-673E1.1"  "RP11-586K2.1" 
## [33] "AB015752.3"    "RP11-624D11.2" "RP11-798K3.2"  "CRTC3-AS1"    
## [37] "LINC00907"     "ARRDC3-AS1"    "RP4-681L3.3"   "RP11-592G13.2"
## [41] "RP11-335E8.3"  "RNF19A"        "ZMAT3"         "RP3-466I7.2"  
## $reactome
##                              category over_represented_pvalue
## 383      glycosphingolipid catabolism            2.177177e-05
## 1019 the activation of arylsulfatases            2.177177e-05
## 384      glycosphingolipid metabolism            1.042914e-04
##      under_represented_pvalue numDEInCat numInCat        FDR
## 383                 0.9999999          3        4 0.01222485
## 1019                0.9999999          3        4 0.01222485
## 384                 0.9999988          3        6 0.03903974
saveRDS(goseq_res, sprintf("output/gene_set_enrichments_%s.RDS", 
                           file_tag))

Session information

gc()
##            used  (Mb) gc trigger  (Mb) limit (Mb) max used  (Mb)
## Ncells  8955031 478.3   16112782 860.6         NA 15734577 840.4
## Vcells 16666523 127.2   31262822 238.6      65536 31262822 238.6
sessionInfo()
## R version 4.2.3 (2023-03-15)
## Platform: aarch64-apple-darwin20 (64-bit)
## Running under: macOS Ventura 13.4.1
## 
## Matrix products: default
## BLAS:   /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRlapack.dylib
## 
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
##  [1] goseq_1.50.0           geneLenDataBase_1.34.0 BiasedUrn_2.0.10      
##  [4] fgsea_1.24.0           biomaRt_2.54.1         limma_3.54.2          
##  [7] tidyr_1.3.0            ggpubr_0.6.0           ggplot2_3.4.2         
## [10] data.table_1.14.8     
## 
## loaded via a namespace (and not attached):
##   [1] nlme_3.1-162                matrixStats_1.0.0          
##   [3] bitops_1.0-7                bit64_4.0.5                
##   [5] filelock_1.0.2              progress_1.2.2             
##   [7] httr_1.4.6                  GenomeInfoDb_1.34.9        
##   [9] tools_4.2.3                 backports_1.4.1            
##  [11] bslib_0.4.2                 utf8_1.2.3                 
##  [13] R6_2.5.1                    mgcv_1.8-42                
##  [15] DBI_1.1.3                   BiocGenerics_0.44.0        
##  [17] colorspace_2.1-0            withr_2.5.0                
##  [19] tidyselect_1.2.0            prettyunits_1.1.1          
##  [21] bit_4.0.5                   curl_5.0.1                 
##  [23] compiler_4.2.3              cli_3.6.1                  
##  [25] Biobase_2.58.0              xml2_1.3.4                 
##  [27] DelayedArray_0.24.0         rtracklayer_1.58.0         
##  [29] sass_0.4.5                  scales_1.2.1               
##  [31] rappdirs_0.3.3              Rsamtools_2.14.0           
##  [33] stringr_1.5.0               digest_0.6.31              
##  [35] rmarkdown_2.21              XVector_0.38.0             
##  [37] pkgconfig_2.0.3             htmltools_0.5.5            
##  [39] MatrixGenerics_1.10.0       dbplyr_2.3.2               
##  [41] fastmap_1.1.1               rlang_1.1.0                
##  [43] rstudioapi_0.14             RSQLite_2.3.1              
##  [45] BiocIO_1.8.0                jquerylib_0.1.4            
##  [47] generics_0.1.3              jsonlite_1.8.4             
##  [49] BiocParallel_1.32.6         dplyr_1.1.2                
##  [51] car_3.1-2                   RCurl_1.98-1.12            
##  [53] magrittr_2.0.3              GO.db_3.16.0               
##  [55] GenomeInfoDbData_1.2.9      Matrix_1.6-4               
##  [57] Rcpp_1.0.10                 munsell_0.5.0              
##  [59] S4Vectors_0.36.2            fansi_1.0.4                
##  [61] abind_1.4-5                 lifecycle_1.0.3            
##  [63] stringi_1.7.12              yaml_2.3.7                 
##  [65] carData_3.0-5               SummarizedExperiment_1.28.0
##  [67] zlibbioc_1.44.0             org.Hs.eg.db_3.16.0        
##  [69] BiocFileCache_2.6.1         grid_4.2.3                 
##  [71] blob_1.2.4                  parallel_4.2.3             
##  [73] crayon_1.5.2                lattice_0.20-45            
##  [75] splines_4.2.3               Biostrings_2.66.0          
##  [77] cowplot_1.1.1               GenomicFeatures_1.50.4     
##  [79] hms_1.1.3                   KEGGREST_1.38.0            
##  [81] knitr_1.44                  pillar_1.9.0               
##  [83] GenomicRanges_1.50.2        rjson_0.2.21               
##  [85] ggsignif_0.6.4              codetools_0.2-19           
##  [87] stats4_4.2.3                fastmatch_1.1-3            
##  [89] XML_3.99-0.14               glue_1.6.2                 
##  [91] evaluate_0.20               png_0.1-8                  
##  [93] vctrs_0.6.2                 gtable_0.3.3               
##  [95] purrr_1.0.1                 cachem_1.0.7               
##  [97] xfun_0.39                   broom_1.0.4                
##  [99] restfulr_0.0.15             rstatix_0.7.2              
## [101] tibble_3.2.1                GenomicAlignments_1.34.1   
## [103] AnnotationDbi_1.60.2        memoise_2.0.1              
## [105] IRanges_2.32.0